Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

Plant Methods

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[1] 0000 0001 2171 2558, grid.5842.b, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Sciences Plant Saclay, 91198, Gif sur Yvette Cedex, France;0000 0001 2171 2558, grid.5842.b, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Sciences Plant Saclay, 91198, Gif sur Yvette Cedex, France;0000 0001 2149 7878, grid.410511.0, Unité de Formation et de Recherche Sciences et Technologie, Université Paris-Est Créteil Val de Marne, 94010, Créteil, France;0000 0001 2171 2558, grid.5842.b, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Sciences Plant Saclay, 91198, Gif sur Yvette Cedex, France;0000 0001 2190 4373, grid.7700.0, Centre for Organismal Studies (COS), Universität Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany;0000 0001 2287 9755, grid.463926.c, LMS, Ecole Polytechnique, CNRS, Palaiseau, France;0000 0001 2186 3954, grid.5328.c, Inria, Université Paris-Saclay, Palaiseau, France;

关键词: Root hair;    Image analysis;    Cell elongation;    Root;    Phenotyping;    Medicago truncatula;   

DOI  :  10.1186/s13007-019-0483-z

来源: publisher

【 摘 要 】

BackgroundThe root is an important organ for water and nutrient uptake, and soil anchorage. It is equipped with root hairs (RHs) which are elongated structures increasing the exchange surface with the soil. RHs are also studied as a model for plant cellular development, as they represent a single cell with specific and highly regulated polarized elongation. For these reasons, it is useful to be able to accurately quantify RH length employing standardized procedures. Methods commonly employed rely on manual steps and are therefore time consuming and prone to errors, restricting analysis to a short segment of the root tip. Few partially automated methods have been reported to increase measurement efficiency. However, none of the reported methods allow an accurate and standardized definition of the position along the root for RH length measurement, making data comparison difficult.ResultsWe developed an image analysis algorithm that semi-automatically detects RHs and measures their length along the whole differentiation zone of roots. This method, implemented as a simple automated script in ImageJ/Fiji software that we termed Root Hair Sizer, slides a rectangular window along a binarized and straightened image of root tips to estimate the maximal RH length in a given measuring interval. This measure is not affected by heavily bent RHs and any bald spots. RH length data along the root are then modelled with a sigmoidal curve, generating several biologically significant parameters such as RH length, positioning of the root differentiation zone and, under certain conditions, RH growth rate.ConclusionsImage analysis with Root Hair Sizer and subsequent sigmoidal modelling of RH length data provide a simple and efficient way to characterize RH growth in different conditions, equally suitable to small and large scale phenotyping experiments.

【 授权许可】

CC BY